BY MOLLIE ZIEGLER HEMINGWAYRobert Ingersoll and his partner, Curt Freed, were longtime customers of Barronelle Stutzman, a florist in Richland, Wash. After voters in the state approved same-sex marriage in December 2012, Messrs. Ingersoll and Freed decided to tie the knot, and called their florist. "There was never a question she'd be the one to do our flowers," Mr. Ingersoll told the Tri-City Herald. But Ms. Stutzman declined, citing her Christian beliefs about marriage. "You have to make a stand somewhere in your life on what you believe and what you don't believe," Ms. Stutzman told Christian Broadcasting Network. For acting on her religious beliefs, Ms. Stutzman has been sued twice: once by state Attorney General Bob Ferguson and once by the American Civil Liberties Union. It wasn't supposed to be this way. Voters were assured that legalizing gay marriage wouldn't undermine religious freedom—after all, the public was assured that religious institutions would be free to act as they always had. But what about religious individuals? The effects of this new legal regime on private citizens have largely been ignored. When the Supreme Court struck down the Defense of Marriage Act in June, President Obama said: "How religious institutions define and consecrate marriage has always been up to those institutions. Nothing about this decision—which applies only to civil marriages—changes that." That line was echoed by the media, with a typical comment coming from the Los Angeles Times editorial page: "Government entities in California must now recognize and extend equal rights to same-sex marriages, but that requirement does not extend to religions, their houses of worship or their ministers." Reassuring words like those may help explain why many Americans support legal recognition for same-sex marriage even though the practice is contrary to their own religious beliefs. Some 97.6% of religious adherents in the U.S.—more than half the population—belong to religious bodies that affirm the traditional definition of marriage, according to the Becket Fund for Religious Liberty. For those Americans, tolerance isn't turning out to be a two-way street. A couple that owns a bakery in Gresham, Ore., closed its shop earlier this month after the state launched an investigation into their religious objections to catering same-sex union celebrations. The New Mexico Supreme Court ruled in August that Elane Photography violated the state's Human Rights Act by declining to photograph a lesbian commitment ceremony because doing so would present a religious conflict. A judge upholding a $6,637 fine against the small business owned by a Christian couple said being "compelled by law to compromise the very religious beliefs that inspire their lives" was "the price of citizenship." Members of the clergy who object to performing same-sex marriages are generally protected from such legal harassment—a fact that advocates for gay marriage emphasized to give the public confidence that religious beliefs would not be trampled by legalization. In 2008, the California Supreme Court suggested that religious freedom would be unaffected by same-sex marriage because "no religious officiant will be required to solemnize a marriage in contravention of his or her religious beliefs." But the protection of the beliefs held by church officials and congregations is guaranteed by the First Amendment and a host of legal precedents. What's at stake is personal religious liberty. "Individuals really haven't gotten much protection at all," says Robin Fretwell Wilson, a professor of the University of Illinois College of Law who lobbies legislatures to protect individual religious liberty when revising marriage laws. It's not just religious-minded business owners who need to worry. County recorders, magistrates and judges in Iowa as well as justices of the peace in Massachusetts and town clerks in New York have been told that refusing to perform services for same-sex couples will result in criminal prosecutions for misdemeanors or other sanctions. Faced with choosing between their jobs and their religious beliefs, many have resigned, including a dozen Massachusetts justices of the peace. "Wherever government is giving you access to something, licensing the power to perform certain acts, government can abuse that position to promote a particular point of view," says Eric Rassbach, deputy general counsel at the Becket Fund for Religious Liberty. Long before the lawsuits, fines and penalties started piling up, many legal scholars recognized that gay rights and individual religious liberty were on a collision course. In 2006, Chai Feldblum, a legal scholar and gay-rights activist later appointed by President Obama to the Equal Employment Opportunity Commission, acknowledged the conflict: "There can be a conflict between religious liberty and sexual liberty, but in almost all cases the sexual liberty should win because that's the only way that the dignity of gay people can be affirmed in any realistic manner." It is only now becoming clear to many Americans what sort of compromise has been imposed on them.Ms. Hemingway is a writer in Virginia.A version of this article appeared September 19, 2013, on page A13 in the U.S. edition of The Wall Street Journal, with the headline: Gay Marriage Collides With Religious Liberty.